A comparative study on methods of optimal sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization mass spectrometry

Metal adducts (e.g., Na+ and K+) significantly hinder the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Although a number of sample purification methods exist, to date no comparative study exists to determine the most efficient method for purifying oligonucleotides. The objective of this work was to perform such a study. Several different oligonucleotide samples were synthesized. Aliquots of these samples were then purposely contaminated with sodium acetate to generate representative contaminated (salted) oligonucleotide samples. A number of popular oligonucleotide purification techniques were then tested as to their effectiveness at removing Na+ from the salted samples. The effectiveness of Na+ removal was qualitatively assessed by comparing the MALDI mass spectra of the original sample, the salted sample, and the salted sample after purification. Micropipet tips packed with C18 reversed-phase packing material (e.g., Zip Tips) appear to be the most effective means of purifying the oligonucleotides investigated. Minidialysis was found to be an effective alternative for purifying higher molecular weight oligonucleotides (> 10,000 u).